Contacts of the strand formed by residues 161 - 166 (chain 3) in PDB entry 3EXG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 161 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843 HIS* 3.4 14.4 - - + -
853 LEU* 4.6 1.3 - - - -
863 ILE 5.1 1.1 - - - -
1453 GLY* 4.0 13.9 - - - -
1483 ILE* 3.7 28.3 - - + -
1493 ALA* 4.0 25.6 - - + +
1523 CYS* 5.1 0.7 - - - -
1603 VAL* 1.3 82.3 - - - +
1623 LEU* 1.3 65.1 + - - +
1633 THR* 3.9 9.9 + - - +
1883 PRO 3.2 6.5 + - - +
1893 CYS* 3.6 0.7 - - - -
1903 ILE* 2.7 34.1 + - - +
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Residues in contact with LEU 162 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753 LEU* 3.9 23.1 - - + -
793 ILE* 3.8 36.8 - - + -
833 ASP* 5.0 1.1 - - + -
843 HIS 2.7 19.1 + - - +
853 LEU* 3.3 21.2 - - + +
863 ILE* 2.9 29.6 + - - +
1603 VAL* 4.4 7.0 - - + +
1613 CYS* 1.3 79.6 - - - +
1633 THR* 1.3 59.5 + - - +
1643 LEU* 4.0 1.8 - - - -
1903 ILE* 3.5 21.5 - - + -
1923 ILE* 3.8 27.1 - - + -
2373 THR* 4.6 5.8 - - + -
2533 MET* 5.6 0.2 - - + -
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Residues in contact with THR 163 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863 ILE* 3.6 5.1 - - + +
1413 GLN 3.4 25.8 - - - +
1423 VAL* 3.4 33.0 - - + +
1453 GLY* 3.3 24.0 + - - -
1613 CYS* 4.1 3.6 - - - -
1623 LEU* 1.3 75.6 + - - +
1643 LEU* 1.3 60.8 + - - +
1653 TYR* 4.0 2.9 - - - -
1893 CYS* 4.0 9.0 - - - -
1903 ILE 2.8 12.8 + - - -
1913 PHE* 3.5 10.3 - - + -
1923 ILE* 2.8 23.8 + - - +
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Residues in contact with LEU 164 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753 LEU* 4.4 7.4 - - + -
853 LEU* 4.0 23.3 - - + -
863 ILE 3.0 20.7 + - - +
873 THR* 3.8 19.0 - - - +
943 PHE* 3.4 31.9 - - + -
1413 GLN* 2.9 25.5 + - - +
1623 LEU* 4.0 14.8 - - + +
1633 THR* 1.3 74.3 - - - +
1653 TYR* 1.3 62.4 + - - +
1923 ILE* 3.2 23.3 - - + +
1943 GLU* 3.4 29.2 - - + +
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Residues in contact with TYR 165 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 THR* 5.7 0.2 - - - -
883 ALA* 5.2 2.0 - - - +
1393 GLY* 5.6 0.4 - - - -
1413 GLN* 3.7 15.9 - - - +
1423 VAL* 3.9 24.7 - - + -
1633 THR 4.0 4.7 - - - -
1643 LEU* 1.3 79.6 - - - +
1663 GLY* 1.3 64.1 + - - +
1693 ALA* 4.7 6.1 - - + -
1703 ALA* 4.1 18.6 - - + +
1753 ILE* 3.9 22.0 - - + -
1793 TYR* 2.5 31.1 + + - -
1913 PHE* 4.3 10.1 - - + -
1923 ILE 2.9 25.2 + - - -
1933 CYS* 3.2 30.8 - - + +
1943 GLU* 2.8 30.0 + - - -
2133 TYR* 4.8 2.0 + + - +
2163 ARG* 5.7 0.5 - - - +
2523 LEU* 3.6 13.9 - - - +
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Residues in contact with GLY 166 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883 ALA* 5.5 4.4 - - - +
1413 GLN* 5.2 0.2 - - - +
1653 TYR* 1.3 76.8 - - - +
1673 ASP* 1.3 68.1 + - - -
1683 GLY 3.2 2.9 - - - -
1693 ALA* 2.9 23.5 + - - +
1703 ALA 3.4 4.3 + - - -
1933 CYS* 4.3 2.2 - - - -
1943 GLU* 3.3 16.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il